{
    "params": {
        "protein1_fasta": {
            "type": "file",
            "description": "FASTA file for protein 1",
            "default": "/omic/eureka/bioemu/input/trp_cage.fasta",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.protein1_fasta",
            "examples": [
                "/omic/eureka/bioemu/input/trp_cage.fasta"
            ],
            "pattern": ".*\\.fasta$",
            "validation": {},
            "notes": "FASTA file containing the first protein sequence"
        },
        "protein2_fasta": {
            "type": "file",
            "description": "FASTA file for protein 2",
            "default": "/omic/eureka/bioemu/input/villin_headpiece.fasta",
            "required": true,
            "pipeline_io": "input",
            "var_name": "params.protein2_fasta",
            "examples": [
                "/omic/eureka/bioemu/input/villin_headpiece.fasta"
            ],
            "pattern": ".*\\.fasta$",
            "validation": {},
            "notes": "FASTA file containing the second protein sequence"
        },
        "outdir": {
            "type": "folder",
            "description": "Output directory for results",
            "default": "/omic/eureka/bioemu/output",
            "required": true,
            "pipeline_io": "output",
            "var_name": "params.outdir",
            "examples": [
                "/omic/eureka/bioemu/output"
            ],
            "pattern": ".*",
            "validation": {},
            "notes": "Directory where prediction results will be stored"
        },
        "complex_name": {
            "type": "string",
            "description": "Name for this protein complex",
            "default": "protein_complex",
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.complex_name",
            "examples": [
                "protein_complex"
            ]
        },
        "num_samples": {
            "type": "integer",
            "description": "Number of protein structure samples",
            "default": 10,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.num_samples",
            "examples": ["10"],
            "pattern": "^\\d+$",
            "validation": {"min": 1},
            "notes": "More samples provide better coverage of conformational space"
        },
        "temperature": {
            "type": "integer",
            "description": "Temperature (K) for free energy calculations",
            "default": 300,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.temperature",
            "examples": ["300"],
            "pattern": "^\\d+$",
            "validation": {"min": 200, "max": 500},
            "notes": "Temperature in Kelvin"
        },
        "n_clusters": {
            "type": "integer",
            "description": "Number of conformational clusters",
            "default": 5,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.n_clusters",
            "examples": ["5"],
            "pattern": "^\\d+$",
            "validation": {"min": 2}
        },
        "exp_dG": {
            "type": "number",
            "description": "Experimental binding free energy (kcal/mol)",
            "default": -10.0,
            "required": false,
            "pipeline_io": "parameter",
            "var_name": "params.exp_dG",
            "examples": ["-10.0", "-13.1"],
            "notes": "Reference experimental value for comparison"
        }
    }
}